Single-cell studies have begun to reveal an unexpectedly dynamic picture of cellular regulation that was previously obscured by traditional techniques that average over cell populations. In particular, diverse systems appear to use dynamic, pulsatile activation mechanisms to control processes such as stress response and differentiation. In such systems, transcription factors are activated in a sustained sequence of discrete and apparently stochastic pulses. Inputs to these systems modulate the frequency, duration, or amplitude of pulses to control downstream processes. The potential generality of pulsatile regulation provokes the general questions of how pulse modulation systems work, what functions they provide cells, and how they interact with one another in the same cell. We will address these questions in Bacillus subtilis, because it contains multiple circuits that use pulsing, often simultaneously, to regulate key stress responses, including the initiation of sporulation. Experimental approaches combine quantitative time-lapse fluorescence microscopy, circuit re- wiring and transplantation, and optogenetic manipulation of kinases, all in close connection with mathematical modeling of the underlying genetic circuits. Using these techniques we will first analyze how pulsed phosphorylation of the master transcription factor Spo0A enables cells to defer the initiation of sporulation for multiple cell cycles in response to sudden nutrient limitation, and use an engineered light activated kinase to analyze the effects of alternative pulse dynamics. We will then study the way in which the general stress response system of B. subtilis, mediated by the alternative sigma factor B, integrates distinct inputs which individually generate different pulse modulation responses. We will reconstitute this system in E. coli to identify a minimal circuit sufficient for frequency encoding of signals. Finaly, we will study alternative sigma factor dynamics more broadly, to understand how and why cells regulate many sigma factors in a pulsatile fashion simultaneously in the same cell. In particular, we will test the hypothesis that parallel pulse-regulation enables these regulators to effectively 'time-share' the limiting resource of RNA polymerase. Together these results will provide a comprehensive approach to understand the role of stochastic pulsing in bacterial cells and identify more general pulse-based design principles applicable across species and cell types. PUBLIC HEALTH RELEVANCE: The spread of infectious diseases depends on the activation of alternative bacterial stress response programs including bacterial sporulation and programs mediated by diverse alternative sigma factors. Recent work has revealed that many such systems are activated in a pulsatile, rather than a continuous, fashion, exhibiting stochastic bursts of activity. This proposal will address the mechanism, function, and generality of this pulsatile mode of regulation. The results will be relevant both for microbial physiology underlying infectious diseases as well as for understanding key regulatory pathways in multicellular organisms.